For what it's worth, the genome assembly software ABySS uses exactly
this system that Jody is describing to represent a directed graph.
http://www.bcgsc.ca/platform/bioinfo/software/abyss
Cheers,
Shaun
jody wrote:
Hi Barnabas
As far as i know, Open-MPI is not a shared memory system.
Using Op
Hi Eugene and Jody,
thanks for the ideas and elaborate answers. I will look into SysV and
mmap, and find out something. I am not tied to PGAPack, there may be
other PGA libs too... But I guess MPI and SysV/mmap do not cancel each
other out, I just have to know about what is running locally and wha
Barnabas Debreczeni wrote:
I am using PGAPack as a GA library, and it uses MPI to parallelize
optimization runs. This is how I got to Open MPI.
Let me see if I understand the underlying premise. You want to
parallelize, but there are some large shared tables. There are many
different para
Hi Barnabas
As far as i know, Open-MPI is not a shared memory system.
Using Open-MPI to attack your problem on N processors, i would poceed
as follows:
- processor 0 reads the table and then splits it into N parts
(Table_0,...Table_N)
- processor 0 sends Table_i to processor i (for all i > 0) usi
